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Molecule Parameter List for Tn | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | | Chemotaxis | 55 | Pathway |
Chemotaxis | | All parameters used are from the .BCT files for BCT1.1 provided by Matthew Levin from the Computational Biology Group in the Department of Zoology at the University of Cambridge.Bias does not reach 0.7, there is a lag in the response of bias to the 5 sec 1 uM Aspartate pulse as shown by Bray et al. Mol.Biol.Cell (1993) 4(5): 469-482. The June 2003 version of the BCT program is BCT4.3 and is available at the computational biology site of the Zoology department at Cambridge University. |
Tn acting as a Molecule in Chemotaxis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Tn | Chemotaxis
Accession No. : 55 | Chemotaxis
Pathway No. : 226 | 0 | 1.41 | No | | Ni bound Tar Ni-Tar = 0 M As per Signal 4 in 1SIG_B.BCT provided by Matthew Levin Cell volume = 1.41e-15 L Table 1 pp.474 Bray et al 1993, Mol.Biol.Cell 4: 469-482 |
Tn acting as a Substrate in a reaction in Chemotaxis Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| | Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | 1 | Complexing[1] | Chemotaxis
Accession No. : 55 | Chemotaxis
Pathway No. : 226 | 0.1
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 10.0003(uM) | - | Substrate
CheW
Tn
Product
TnW
| | | Nickel bound Tar and CheW complex TnW = 0.0 uM As per Signal 8 in 1SIG_B.BCT provided by Matthew Levin Cell volume = 1.41e-15 L Table 1 pp.474 Bray et al 1993, Mol.Biol.Cell 4: 469-482 | | 2 | Binding[4] | Chemotaxis
Accession No. : 55 | Chemotaxis
Pathway No. : 226 | 0.05
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 19.9999(uM) | - | Substrate
CheA
Tn
Product
TnA
| | | Bias calculated as per formula stated on pp.471 Bias = [M + MYp] / [M + MYp + MYpYp + MYpYpYp + MYpYpYpYp] Bray et al 1993, Mol.Biol.Cell 4: 469-482 Initialy set to 0.7 | | 3 | Binding[10] | Chemotaxis
Accession No. : 55 | Chemotaxis
Pathway No. : 226 | 0.4
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 2.5(uM) | - | Substrate
Tn
WA
Product
TnWA
| | | Binding of Tn and CheW-CheA complex Kf = 4e+05 /sec/M = 0.4 /sec/uM Kb = 1 /sec Bray et al 1993, Mol.Biol.Cell 4: 469-482 Table 3 pp.476 Reaction Scheme 8 Footnote states that ligands do not have any effect on the formation of complexes so same rates are used for Aspartate or Ni associated Tar complexes. |
Tn acting as a Product in a reaction in Chemotaxis Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | Binding | Chemotaxis
Accession No. : 55 | Chemotaxis
Pathway No. : 226 | 0.001
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 1000.028(uM) | - | Substrate
Ni
Tar
Product
Tn
| | Binding of Tar and Ni Kf = 1 * 10e+03 /sec/M = 0.001 /sec/uM Kb = 1 /sec Bray et al 1993, Mol.Biol.Cell 4: 469-482 Table 3 pp.476 Reaction Scheme 2 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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